Hello all,
When I am reading papers, I always read this:
The substrate includes three kinds of atoms: boundary atoms, thermostat atoms and Newtonian atoms in the course of MD simulations. Three layers of atoms at the bottom of the substrate (lower z plane) are boundary atoms. The next six layers of atoms adjacent to the boundary atoms are thermostat atoms. The motions of thermostat atoms and Newtonian atoms obey the classical Newton’s second law. The Newton’s equations of motion are integrated with a velocity-Verlet algorithm with a time step of 1*10^15 s. Periodic boundary conditions are imposed in the x and y direction for all simulations.
The constructed single crystal model is relaxed using an energy minimization with a conjugate gradient method, followed by a zero-stress relaxation in the isothermal?Cisobaric ensemble (constant number of particles, pressure, and temperature, NPT) using a Nosé?CHoover thermostat at 300 K for 20 ps (20,000 steps). In order to bring the GB-containing system closer to reality, the bicrystal model is heated to 900 K for 100 ps and then gradually cooled down to room temperature (300 K). An equilibrium initial configuration is obtained after relaxation.
[Sun et al_2013_Atomistic scale tribological behaviors in nano-grained and single crystal.pdf]
How to write LAMMPS’ in script, I has defined this:
group workpiece_Cu region workpiece_Cu
group newtonian_layer region newtonian_layer
group thermostat_layer region thermostat_layer
group boundary_layer region boundary_layer
But I do not how to write others. Can anyone help me? Thx inadvance.
Best regards.